Jonas Quinn is now the fourth member of SG-1. Their first mission is to investigate an abandoned Ha'tak vessel orbiting Earth. They investigate and figure out that it belonged to Anubis, and the consciousness of Thor caused the ship to malfunction. Furthermore, the ship is heading down towards the Pacific Ocean.
The Kelownans, Jonas Quinn's people, want to re-establish trade relations with the Tau'ri. Jonas is offered clemency in exchange for spying on his old mentor, Dr.Kieran, who claims to form a resistance to take away all of the Naquadria.
The Goa'uldKhonsu has learned of SG-1's location and has his Jaffa capture the team. SG-1's only hope to rescue them is the incompetent scientist Dr.Jay Felger, who is quite fond of the team, but his mission is soon unsurprisingly compromised.
SG-1 arrives on Pangar, where the inhabitants have created a drug called Tretonin to cure all ailments. They soon realize that Tretonin is actually made of Goa'uldsymbiotes. In a twist of fate, SG-1 learns that it is not a Goa'uld queen making the symbiotes, but a Tok'ra.
After retaking the new ship Thor asks SG-1 for their help in defeating the Replicators once and for all, since the Replicators have taken over Hala and have taken Human form. The only way to ensure the success of taking them down is to trust Fifth, one of the Replicators.
After returning from a planet, Jonas Quinn is startled to see some bugs that no one else can see. Soon other SGC personnel also start seeing the bugs. Attempts to contain the situation go badly and civilians start seeing them also.
SenatorRobert Kinsey is shot by an assassin, who later turns out to be ColonelJack O'Neill. As a result he is arrested even though he says he was nowhere near the scene at the time. The rest of the team investigate who is framing him.
Harold Maybourne leads SG-1 to an arch on another planet, where he transports himself to "paradise". Unfortunately, ColonelJack O'Neill is also stuck with him. As they have to cope with each other, MajorSamantha Carter tries her best to find the two. Meanwhile, O'Neill suspects Maybourne is starting to act paranoid.
Nirrti makes a return when SG-1 finds her continuing her experiments on enhancing evolution on the residents of the planet P3X-367 . SG-1 and the RussianSG-4 are sent to stop her. However, her 'experiments' do not want SG-1 to kill her, and she gives Jonas Quinn an irresistible offer.
SG-1 find the crew of the ship Sebrus on an abandoned planet, but there are also a group of aliens after them. SG-1 tends to them, but not all is as what it seems, as Jonas Quinn uncovers about the background of the Sebrus from Earth history.
The Prometheus'hyperdrive is ejected when the drive's Naquadria becomes unstable, and the Prometheus lands on a planet named Tagrea. The crew cannot contact Earth for help because the planet's Stargate is buried, and they have to find it. However, the planet's military leader has other plans.
Mot is planning on taking over a planet of poor inhabitants. Meanwhile, Jonas Quinn, who was experimented on by Nirrti, receives a series of startling visions about what is going to happen, including the destruction of Stargate Command. He plans on stopping this, but the visions are slowly killing him.